Ancillary Sword: People know that something is wrong when Breq doesn't sing - this is despite her singing voice being implied to be rather bad. It's such a common background noise that it unsettles people when the singing stops. Another example is when Lieutnant Tisarwat acts in a way that seems to be out of character for the person reports on her imply her to be. Breq gets suspicious. Turns out she is right; Tisarwat has been given implants that removed her own personality and replaced it with that of Aanaander Minaai, effectively making her a body part of the lord of Radch space.
Mac The Bartender is also The Quiet One. The seriousness of any particular book is proportional to the number of words that he says. A complete sentence or two is enough to scare Dresden. In Changes he goes on for a good sized paragraph.
Also, in Blood Rites, Lieutenant Murphy meets Harry's mentor, Ebenezer McCoy. As they are on a hunt for vampires in Chicago, Murphy tells him (rudely) to get out of the driver's seat. Harry tells him to do it, slipping in the word "sir". Murphy drops everything she's carrying, mainly because hearing the anti-authority Dresden using the word "sir" is something that you only hear once. Also justified, as Ebenezer is the only one to whom Harry will apply an honorific. Being Harry's mentor has its perks. Murphy then asks Ebenezer again, but this time, she asks politely.
In Dead Beat, Harry asks Bob about Kemmler, the author of a book that the visiting group of Necromancers are all hot and bothered about. Bob has a minor freak-out, and tells Harry that Kemmler was straight up, capital-E Evil. This immediately catches Harry's attention, mainly because Bob's view on morality is... sketchyat best. This happens again later in the book when Harry talks to Mab, Queen of Air and Darkness of the Winter Sidhe, who also calls Kemmler a madman and a monster—which makes an impression coming from someone who Harry knows has spent more than three years on the last person who betrayed her, crucifying him the entire time.
Toot-toot the dewdrop faerie is normally fearless and a ravenous junk-food addict. When Toot tells Harry to run, it's serious; when he tells Harry to forget the doughnut and run, it's dreadfully-so.
The one time in his life that Morgan calls Harry by his first name is when he tells Harry to stand down and let the Wardens arrest Morgan for murder, rather than get himself killed defending a man he knows to be innocent.
Two incidents related to Harry himself and mental magic: In White Night, Murphy points out that he's been flying into a rage and burning things more than usual lately, which points out how Lasciel has been influencing him subtly. In Small Favor, Harry spends most of the book getting into sticky situations full of monsters and notincinerating them out of hand. This is because Queen Mab removed his memory of how to do so (and took away his blasting rod for good measure), ostensibly for his own good.
To Kill a Mockingbird is full of these: Scout notes the only time she ever heard Atticus raise his voice (when he's defending his parenting style to Aunt Alexandra) and the only time she ever heard him call something a sin (to kill a mockingbird). Jem decides to follow Atticus the night the mob threatens him outside the jail because Atticus took his car instead of walking as usual. Scout and Jem are shocked at Tom Robinson's trial when Atticus takes off his jacket and loosens his tie, because they've never seen him do that during the day. Scout knows that Aunt Alexandra is seriously shaken when the children have been attacked at the end, because she brings Scout her overalls to put on, after spending the entire book trying to get her to stop wearing them. And, of course, there's Boo Radley leaving his house for the only time in living memory in order to protect them from Bob Ewell.
The plot kicks off when Shelena encounters a shaggy, nocturnal predator, in the middle of the road in the middle of the day. Instead of showing off first as any shaggy would do before a fight, he attacks her immediately, and thus she begins her investigation.
Veres is seriously freaked out when Shelena throws him on the bed and starts smooching and undressing him in the middle of investigating the room. Turns out, somebody was watching them and she feigned the effects of love potion to get him to lower his guard.
In the earlier books, moments when Hermione was in favor of breaking the rules were this.
Most notable was when Harry and Ron save Hermione from a cave troll. She saves them from getting into trouble by lying and saying she thought of going after the troll and they were only rescuing her (when really, the troll found her by chance and Harry and Ron broke the rules and went after it, instead of going to their dormitories). Not only did Hermione lie to a teacher to cover for Harry and Ron's rulebreaking (something which she refused to go along with earlier), but she used a cover story that made her out to be the rulebreaker. Harry compares the situation to Snape giving out candy.
In Prisoner of Azkaban, Hermione slaps Malfoy across the face for insulting Hagrid. It scares Malfoy enough to shut him up and get him to leave.
A rather terrifying example happens at the end of the first book. when Harry finds p-p-poor s-stuttering Professor Quirrell in front of the Mirror of Erised — and he isn't stuttering...
In Prisoner of Azkaban, Dumbledore loses his temper for the first time in the series when a pack of Dementors nearly kill Harry. Hermione mentions that it was absolutely terrifying.
And again when confronting the fake Moody in The Goblet of Fire - Harry realizes just how much of a threat Dumbledore is to the Death Eaters, as he sees for the first time that Dumbledore isn't just a harmless old man, but is a powerful and dangerous wizard capable of magic that Harry can't even pronounce.
Sweet, motherly Molly Weasley reacts rather badly when Bellatrix nearly kills Ginny.
In The Order of the Phoenix, Fred and George (who had previously gotten revenge via subtle trickery) began punching Malfoy in front of the school after a Quidditch match, because he was insulting their parents. Meanwhile, one of the things that truly breaks Ron out of his snarky, laid-back personality is hearing someone insult his family, Harry, or Hermione.
A rather frightening example happens in Deathly Hallows, where it turns out that the corrupting power of Horcruxes can cause this sort of thing to happen. Between a combination of low self-esteem and his wearing the locket, Ron sinks into a suspicious, depressed state which in turn dampens the hope of Harry and Hermione.
Another one in Deathly Hallows is when Lupin, who is usually the calm voice of reason, starts shouting about how he should never have married Tonks, how guilty he feels about potentially passing on his condition to his unborn child, and how his new family will be much better off without a father and husband they should be ashamed of. Fortunately, a What the Hell, Hero? from Harry sets him back on track, but it's quite jarring to see just how low an opinion of himself Lupin has, especially since he's one of Harry's few remaining parental figures and looked up to by a great number of other characters.
As long as we're talking about Deathly Hallows, let's remember Hermione's out-of-character actions, too: First she uses the "Muffliato" Charm (which she used to disapprove of in the past due to its inventor) to help the trio better hide their tracks, especially once they have to go on the run; then, during the Battle of Hogwarts, at one point she asks Harry to utilize his Psychic Link with Voldemort to gain access into his thoughts — something she always preferred Harry to avoid and block out whenever possible before then — in order to find out Voldemort's location so the trio can seek him out and proceed with their destruction of the Horcruxes.
The Lord of the Rings: When Aragorn is presented in the book, even before we know his real name, he seems tough and collected, and you have to read the books a number of times before you get this, but he definitely cracks up a moment when he is trying to explain the very real terror of the Nazgûl. For a badass like Aragorn, hardened by decades of trekking unpleasant areas and encountering all kinds of animals, this comes down as a warning that the ringwraiths should be feared.
For that matter, Legolas when he recognizes the balrog. He just drops his weapon and laments.
In The Chronicles of Narnia series, this happens in The Voyage of the Dawn Treader. When the ship is attacked by a giant sea serpent, Reepicheep yells at everyone to push the serpent off the boat rather than fight it. Since Reepicheep usually leaps at any opportunity for glory in battle (at one point earlier in the book he had to be restrained from challenging a dragon to single combat), this is unusual enough to startle the rest of the ship's crew into helping him.
In Roadkill, the fifth book of the Cal Leandros series, Robin Godfellow, aka lust incarnate, seriously considers becoming monogamous. All of his friends instantly assume he must be seriously ill.
Rincewind is an inept coward who would much rather run away from most problems rather than face them head-on. In Sourcery, Rincewind challenges the most powerful source of magic on the disc with a half brick in a sock, and then holds off a swarm of eldritch abominations long enough to escape, armed with only a sock full of sand.Holy shit.
Conversed by Twoflower in The Light Fantastic, when he reasons that Rincewind's uncharacteristic lack of fear about the Red Star implies that it's not the world-ending threat most people assume it to be.
He does it again in Interesting Times, when faced with the horrors of the Agatean Empire. Rincewind concludes that there are times you have to stop running, even if it's because there's nowhere left to run to.
Death almost never ends his sentences with an exclamation mark, so you know he's pissed off when he shouts at the New Death for setting himself up as a ruler over mortals, in Reaper Man.
This is also invoked for Death when he speaks emphatically of the Auditors' hatred for humanity in Hogfather (represented as italics), shocking Susan.
Death's first major role in Mort, where he is throughout the book made to be The Stoic, and is even explained to lack the physical capability for feelings, but in the climax of the book he expresses extremely human rage, unlike ever before or after, and when Mort is at his mercy, he does a mocking, cruel Evil Laugh, which also is a completely unique expression of negative emotion — right before revealing that he decided to spare Mort and his friends after all.
Vetinari takes pride in his ability to play Sam Vimes like a fiddle and get him to do the best job imaginable... all by keeping him suitably pissed off. Vimes even tends to punch the wall outside Vetinari's office as he leaves, sometimes hard enough to require repair. Until one day Vimes departs, and Vetinari doesn't hear the telltale thump, and realizes that he might have gone too far.
The Librarian hates to be called a monkey (orangutans are apes), and will apply a great deal of physical violence to remind people when they forget this. That's why, when the Senior Wrangler calls him one in The Last Continent and gets away with his head still screwed on, the other wizards become quite concerned.
There's another occasion when someone calls him a monkey, and he pats their hand comfortingly. Although that latter one is because the character in question was so mad that they might have literally out-murdered the Librarian if the Librarian had tried to "correct" him.
In A Hat Full of Sky, Rob Anybody is so worried about the hiver going after Tiffany that he starts to lose interest in hunting, fighting, and other activities typical of the Nac Mac Feegle. When he refuses a drink of Special Sheep Liniment, the other Feegles are briefly convinced he's dead.
In The Fifth Elephant, while searching for Angua, Carrot not only raises his voice when Gaspode tells him a wolf has been caught in a nearby village, but actually uses deception to acquire the animal so it can help them locate her. For straight-laced, inscrutable Carrot, that's tantamount to any other man having a full-on nervous breakdown when his girl goes missing.
In Night Watch, when a young Corporal asks Sgt. Colon where he, Vimes and Nobby (and we find out later, Reg Shoe) are going and why they were all wearing sprigs of lilac. The usually jolly Colon rounds on the youngster and tells him that anyone who had the right to ask that already knew and was headed in the same direction. Vimes has to lead him away to calm him down.
In Making Money Mr. Bent has personally checked every clerk's work with amazing speed and total accuracy for years. When he incorrectly marks one calculation wrong the junior clerk ashamedly looks over it, then pulls out a notebook to work it out on paper, then has one of the senior clerks check his work herself, then she calls over all the other senior clerks to check it as well. Then they write a note saying that the junior clerk appears to be correct and put his work back in Mr. Bent's in-tray, and the room holds its breath while they wait for him to get to it. When he runs out of the building screaming, the entire bank shuts down. Not long after Mr. Bent dresses up as a clown and strangles two would-be assassins with balloon animals.
In Good Omens Aziraphale the angel may no longer be completely uncorrupted by humanity, but he's still angelic enough that he's the undisputed master of Gosh Dang It to Heck!. Then, he swears. And shit just got serious.
Daur is considered the most straitlaced and disciplined of the lot. In Only In Death, he nearly hits Rawne, which is taken as a sign of the insidious effects of Hinzerhaus. In Blood Pact, when he is caught helping out in one of Rawne's scams, Hark thinks that the regiment's discipline and morale has hit a new low.
Only In Death has some more of these. Normally unflappable Mkoll gets spooked, chatty Maggs is unusually silent...
E.E. Smith's Skylark Series: The reason Dick Seaton knows the scientific knowledge he needs to save the Earth exists is because of independently-evolved legends from two worlds of a large and complex star cluster, which describe their gods stunning mortals who attack them. This is despite ten thousand years of strike-to-kill conditioning in both races. Ergo the legends must contain a grain of truth to have lasted for that long without "stunned" being changed to "killed", and the "gods" must be the Sufficiently Advanced Aliens he's looking for. He turns out to be right.
In Larry Niven's short story "Flatlander", our hero Beowulf Shaeffer has just finished doing some scans outside the spaceship. He turns to his companion:
Beowulf: Elephant, have you noticed a tendency in me to use profanity for emphasis? Elephant: No, not really. Beowulf: Well, it's goddamned radioactive out there.
In second The Black Company book, when Goblin doesn't way to play tricks with One-Eye as he usually does and instead of smiling and humilating his rival he actually gets provoked by him — worse, attacks him with his bare hands — everybody knows there is something wrong.
In the first chapter of World War Z, Dr. Kwang Jing-shu says he knew that something very bad was happening through a combination of this trope, Meaningful Echo, and Out-of-Character Alert. An old army comrade renowned for seeing the worst in any given situation, Dr. Gu Wen Kuei, once had a rare non-curmudgeonly moment when they were performing extremely difficult surgery in the middle of a dangerous border clash in Russia, and said to the nearly-disembowelled patient, "Don't worry, everything's going to be all right." Years later, when Jing-shu calls him about a small outbreak of unusual symptoms, Kuei, who knows what's going on, repeats the familiar reassurance, and that's when Jing-shu realizes that the outbreak is not isolated and the situation is much worse than he thought.
Marco is known for being such a fountain of snark that whenever he's serious, it's safe to assume that something pretty upsetting is going on. At one point, during a mission that involved his mother, when he was understandably preoccupied, Jake had to take him aside and tell him to start cracking stupid jokes because he was scaring the others.
Jake did the same thing to Rachel in another book when she was acting too cautious.
Commented on when Ax starts screaming at everyone to book it during an infiltration attempt:
Ax never yells. So when he does, it's usually a good idea to pay attention.
This was how the kids realized that Jake had been made a Controller in book 6: When Ax touches Jake’s cheek, the Yeerk in Jake’s head can’t handle it and screams, “Get your hands off me, Andalite filth!”, thus blowing his cover. He immediately tries to play it off as stress, but the others aren’t having it, and Rachel lampshades it.
The sole time one of the Chee fight, Rachel is later seen crying. This more than anything convinces Marco how horrific the slaughter was.
Very early on Jake's older brother Tom is talking to him about joining The Sharing (A front for the Yeerks) when Jake notices while Tom looks and speaks normally, his eyes are showing pure terror. It's the real Tom warning Jake away.
In the Dark Nest Trilogy, Luke Skywalker (whose job it is to exemplify tranquility and serenity) drops the GFFA equivalent of the F-bomb.
In Warrior Cats, Jayfeather invokes this by saying he's glad that the cranky elder Mousefur isn't acting all sweet and kind because that would mean she was getting heat stroke from the recent hot weather. Later when she starts acting mopey because of Longtail's death, Jayfeather gets really worried about her well-being.
Played for laughs in The Fourth Apprentice, when Blackstar welcomes the journeying cats into his territory with open arms. Lionblaze responds with a snarky "Who are you, and what have you done with Blackstar?"
In the Dale Brown novel Sky Masters, normally composed Jon Masters lets the pressure get to him, up to the point of Rant-Inducing Slight, something his chief assistant notices immediately.
In the final novel of the Codex Alera, Tavi is rather shocked when his lover Kitai becomes furious with him for carrying on a relationship with her without marrying or courting her. Note that Kitai has never given a damn about Aleran laws or customs (or really ever noticed them, except to snark about them) and her own people's view on this sort of thing is rather more... relaxed. So why is she so bent out of shape? She's actually pregnant with her and Tavi's child, and while perfectly happy to flout Aleran rules herself, Kitai does not want her child to have to deal with the major social stigma Alerans place on illegitimacy.
Vivenna from Warbreaker believes that women should dress modestly with high-necked dresses, with skirts that come down to the calf at least. However, when she decides to become more of an Action Girl, she dons a man's trousers and shirt.
Ham from Mistborn spends the better part of three books mired in interminable ponderings, dilemmas, and hypotheticals. Finally he answers a question with "No", and the questioner's response is to ask, in shock, if he really just gave a straight answer. Given the question asked was if there was hope of survival, it's taken seriously.
Honor Harrington is generally portrayed as a military professional: killing is an unfortunate consequence of her career, she takes no pleasure in it, and she can be courteous to former military opponents who tried to kill herbecause that was their job. Those who have known her long enough instantly recognize (and are scared shitless by) her change in bearing when she really, truly wants someone to die. When she discovered that an enemy had not just permitted, but ordered the rape and murder of her subordinates, she turned right around and tried to shoot him. Her friends had to physically hold her down to keep her from killing a prisoner. Later, she legally executed the men who had her lover assassinated in the most painful way she could manage.
When the very anti-killing Campion informs a mook who helped kidnap one of his friends that if she was hurt, he'd "break his rule" and kill him.
In Artemis Fowl, Julius Root apologizing after referring to another fairy as 'human-blooded' is used to convey just how serious an insult 'human-blooded' is amongst fairies. In the second book, the LEP realise just how screwed they are when the usually gung-ho Captain Kelp orders a retreat.
At one point, Artemis (usually very serious and very articulate) calls Butler and simply shouts "Lollipops!" This makes Butler even more worried than he already is.
Artemis's even less fitting "Take Cover" is lampshaded on the spot, as the pair analyze the complete inability of the brilliant but soft Artemis of producing a martial or commanding tone. Not that his typical tone would have been effective anyways, there's really no fast way to convey the concept of the use of a Troll as a breaching tool.
Kitty Norville is a chatterbox by nature who prefers to avoid violence and tries to get any fellow lycanthropes she meets to let the human aspects of their psyches call the shots as much as possible. So when she (in human form, mind you) lunges at an unarmed normal man on sight and does nothing but literally snarl when bodily restrained, the first question out of the mouth of someone that has known her for a couple of days is "What did you do to her?"
In A Series of Unfortunate Events Aunt Josephine is extremely obsessed with grammar. When the Baudelaires find her apparent suicide note Klaus begins to analyze the grammatical errors, but Violet disgustedly asks who would care about grammar in their situation. Klaus points out that Aunt Josephine would and realizes the mistakes are actually a coded message.
In the Paladin of Shadows book A Deeper Blue, Mother Lenka laughing heartily is recalled with horror.
Talen is found to have followed the knights on their mission to Zemoch. When questioned, he stammers and stutters, eventually giving an incredibly unbelievable story about why he followed them. Since Talen has never once been shown to be at a loss for words and has proven the ability to make up believable lies on the spot, this clues the knights in that Aphrael, the Child Goddess, is influencing Talen, since She had wanted him on the mission in the first place and is known to be a horrible liar.
This trope is the clue to Sparhawk that someone is using magic to influence the various kings of Eosia into confining the Pandion knights, as they are believing outlandish claims without any evidence and have turned aggressive towards their allies. It is revealed to be a spell that induces belief being cast by Annias, which is another example because as a church man, he is not permitted to learn magic.
In the sequel saga The Tamuli, whenever Sparhawk stops being his short-tempered self and goes eerily calm, you know shit is gonna go down. The first time it's humorous, when he doesn't yell at Elhana for making it so she'll go to the Tamul Empire—which is currently at the gates of a civil war, although this time it was because Kalten took Sparhawk to a crypt and made him yell and wave his arms there so he'd have a clear head to confront his wife. The second time, less so, since it was caused by the kidnapping of his wife.
At one point Lando Calrissian, teaching Zak about playing cards, tells him "A good rule to follow is that if the other guy is acting normal under unusual circumstances, you can bet he's bluffing".
Army of Terror has The StoicPapa Wolf Uncle Hoole, confronted with the Kivan wraiths menacing him and his charges, just... stop fighting completely, take a Pose of Supplication, and wait for death. When someone else drives them away, he who is so good at Dissonant Serenity is profoundly shaken. He is The Atoner and blames himself for their deaths, just as they blame him.
In Spore, well, here's a quote.
Hoole touched the gash delicately. "I will live." The stern Shi'ido tried to look as light hearted as his stony face could manage. "It was not my best landing, but all things considered, I would say it wasn't my worst." Tash grimaced. Hoole never joked. The fact that he was trying to probably meant he felt worse than he looked.
In LIES, Caine Soren is visibly disturbed by the fact that his girlfriend Diana Ladris A) isn't beautiful anymore and B) Isn't being snarky and sarcastic. He notes that this is a sign that she's finally lost her will to live. Serious business, indeed.
In the same installment of the series, Lana seems to lose hope when she notices Caine isn't being a cocky, arrogant sociopath, actually seeming quite insecure and timid, and remarks; "You gotta give he guy some credit; he has a genius for doing the wrong thing. We actually need him to be the bad guy, and now he's mr. meek and mild."
Devout Catholic Astrid loses her faith in God... And Promptly decides thats a good excuse to throw her brother out a window.
The first sign Alys gets that something is wrong in Terra Mirum Chronicles is that the sheriff arrives at the restaurant she works at an hour ahead of his usual time. It turns out he was at her best friend Charlie's house where Charlie committed suicide the night before.
This is the only way to detect Changed Ones in Hometown. Sometimes the symptoms are subtle, but when the local Big, Friendly Dog starts acting more like a rabid wolverine, you know something's wrong.
In Across the Universe, Amy only knows Elder as a sweet, somewhat awkward teenage boy trying to do his best to lead Godspeed. Therefore, when she suspects he snapped and murdered Luther, in the second book, she is severely shaken at the thought.
Kopaka has a few such moments in the BIONICLE books. First, when believing Pohatu to have died in a cave-in, turns sappy and offers the mask they've been trying to find to Pohatu's people. In a later book, after being beaten by the bad guys, robbed of his mask and tools and attacked by a bunch of innocent villagers mistaking his team for villains, he breaks down and attempts to kill the villagers without hesitation.
When You Reach Me: Wheelie is the school secretary who knows all of the students, what class they are in, and even who is absent. But when the police come looking for Marcus, Miranda realizes just how bad the situation is when Wheelie asks them to repeat his name and ask what grade he is in.
When Ciaphas Cain note Hero of the Imperium!!! realizes that his squad just found a Necron tomb and is giving orders to seal it, he knows that his "everything's under control" mask slipped big time. This actually reinforces his orders to the troopers.
[Grifen] no doubt thought that anything bad enough to leave a hero of the Imperium in need of clean undergarments was something she didn't want to meet.
In fact, anytime Cain thinks Necrons are involved, he is entirely willing to sacrifice his reputation and the luxury that goes with it- the only motivation he will actually go and fight orks, tyranids and Chaos loonies for (or so he claims, he's clearly not the abject coward he describes himself as).
In Murderess, Déaspor and "Hat Lad", who usually have a rather smug and somewhat condescending yet benign attitude, become very angry when Lu or Hallwad and Aucasis refuse to take on their mission.
The Witling takes less than two pages to establish that Parapfu Moragha views Thengets del Prou as a smug, self-satisfied twit. Moragha commissions him to "seng"—to use clairvoyance to scout—an area in the first scene in the book, and Prou claims not to have found anything, but says it without smirking or being snarky; based on this, Moragha correctly guesses that Prou is lying.
In Donnelly's Rogue Wave, while Neela is telling her parents about Abbadon's return, she repeatedly refuses offers of sweets. This furthers their belief that she is mentally ill, as the 'old' Neela had a problem with emotional eating.
In Noob, Arthéon figures out that the new update to the Fictional Video Game he's palying is probably going to make accessible a continent that was so far protected by a Perpetual Storm. One of Arthéon's leads to figure out if he's right is to go pay a visit to the Bold ExplorerNon-Player Character that is known to have mapped the continent's shape and see is the game's update has caused any change of behaviour in him.
Thomas Cromwell breaks down in tears at the end of a year which has seen the death of his wife and daughters and the irrevocable disgrace of his master, Cardinal Wolsey, which threatens to drag him down after he's spent his life trying to build a respectable situation for himself. George Cavendish (another of Wolsey's men) is deeply disturbed when he realizes that Cromwell is crying, and takes this as a sign that there's no hope left for Wolsey.
In a less dire example (or less immediately dire), Cromwell realizes that Henry has actually fallen in love with Jane Seymour when they're chatting about someone's health complaints and Henry declines to go on at length about home remedies like he usually does.